After her proxy marriage to the Prince of Asturias and Louis's proxy marriage to the Infanta Anne, Elisabeth and her brother met their respective spouses for the first time on 25 November 1615 on the Pheasant Island in the river Bidassoa that divides France and Spain between the French city of Hendaye and the Spanish city of Fuenterrabía. This was the last time Louis would see his sister. In Spain, Elisabeth's French name took on the Spanish form of Isabel. The religious ceremony took place in the Saint Mary Cathedral in Burgos. At the time of her marriage, the thirteen-year old Isabel became the new Princess of Asturias.

In 1621, by the time of the birth of the couple's first child, the couple had ascended to the throne of Spain upon the death of Philip III of Spain. The new queen of Spain was aware that her husband had mistresses {Memoirs of Madame de Mottville}

Elisabeth herself was the subject of rumors about her relations with the noted poet Peralta (Juan de Tassis, 2nd Count of Villamediana), who was her gentleman-in-waiting. On 14 May 1622, a fire broke out while the Peralta masqueLa Gloria de Niquea was being acted before the court. Peralta carried the queen to a place of safety, which caused suspicion of their relations to deepen. Peralta neglected a significant warning that his life was in peril, and "he was murdered as he stepped out of his coach. The responsibility for his death was divided between Philip IV and Olivares" (at the time, Prime Minister and King's favorite).

Elisabeth's last child, Infanta Maria Theresa of Spain, would later become Queen of France as the wife of her nephew, the future Louis XIV. Unlike her husband and sister-in-law, she would not see the wedding that cemented the peace between her homeland and adopted country, Spain; the countries would be at war until 1660.

Coat of Arms of Elisabeth of France as Queen Consort of Spain

Elisabeth was renowned for her beauty, intelligence and noble personality, which made her very popular with the Spanish people. She was regent of Spain during the Catalan Revolt and supported the Duke of Nochera against the Count-Duke of Olivares in favor of an honorable withdrawal from the Catalan Revolt.

* also an infanta of Spain by marriage
** also a princess of Tuscany by marriage
*** also a princess of Modena by marriage
^also an archduchess of Austria in her own right
^^did not have a royal or noble title by birth

* also an infanta of Portugal by birth,** also an infanta of Spain and an archduchess of Austria,*** also an infanta of Portugal by birth and an infanta of Spain,**** also an infanta of Spain,***** also a princess of Saxe-Coburg and Gotha, Duchess in Saxony,****** status disputed